The Deep Scan is a feature of the product that performs an extensive (in depth) scan of the Windows Registry.

How does the Deep Scan differ from the other areas of scanning?

The Deep Scan option looks for registry errors in areas of the Windows Registry that aren't already listed among the 10 sections you see in the Scan section. In fact, most registry cleaners in the market generally limit their products to these generic sections and don't go any further.